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<h1><a href="https://archiveofourown.org/works/23636269">rogue</a> by <a class='authorlink' href='https://archiveofourown.org/users/nonbinaryezrabridger/pseuds/nonbinaryezrabridger'>nonbinaryezrabridger</a></h1>

<table class="full">

<tr><td><b>Series:</b></td><td>stargate trope bingo [4]</td></tr>

<tr><td><b>Category:</b></td><td>Stargate Atlantis</td></tr>

<tr><td><b>Genre:</b></td><td>Gen, Independent Atlantis, don’t copy to other sites</td></tr>

<tr><td><b>Language:</b></td><td>English</td></tr>

<tr><td><b>Status:</b></td><td>Completed</td></tr>

<tr><td><b>Published:</b></td><td>2020-04-13</td></tr>

<tr><td><b>Updated:</b></td><td>2020-04-13</td></tr>

<tr><td><b>Packaged:</b></td><td>2021-05-02 19:47:43</td></tr>

<tr><td><b>Rating:</b></td><td>Teen And Up Audiences</td></tr>

<tr><td><b>Warnings:</b></td><td>No Archive Warnings Apply</td></tr>

<tr><td><b>Chapters:</b></td><td>1</td></tr>

<tr><td><b>Words:</b></td><td>2,651</td></tr>

<tr><td><b>Publisher:</b></td><td>archiveofourown.org</td></tr>

<tr><td><b>Story URL:</b></td><td>https://archiveofourown.org/works/23636269</td></tr>

<tr><td><b>Author URL:</b></td><td>https://archiveofourown.org/users/nonbinaryezrabridger/pseuds/nonbinaryezrabridger</td></tr>

<tr><td><b>Summary:</b></td><td><div class="userstuff">
              <p>Woolsey tries to replace Sam as commander of Atlantis. No one expected her and the whole of Atlantis to go rogue in response.</p>
<p>(Independent Atlantis AU)</p>
            </div></td></tr>

<tr><td><b>Series:</b></td><td>stargate trope bingo [4]</td></tr>

<tr><td><b>Series URL:</b></td><td>https://archiveofourown.org/series/1698106</td></tr>

<tr><td><b>Comments:</b></td><td>4</td></tr>

<tr><td><b>Kudos:</b></td><td>83</td></tr>

</table>

<a name="section0001"><h2>rogue</h2></a>
<div class="story"><div class="fff_chapter_notes fff_head_notes"><b>Author's Note:</b><blockquote class="userstuff">
      <p>Written for the "independent Atlantis" square on my stargate trope bingo.</p>
<p>this isn't as long as i wanted it to be but i ran out of inspiration, so...</p>
<p>tw for this story:</p>
<p>mentions of death</p>
<p>the ability to block the wormholes from forming by tilting an iris or shield into the gate is taken from the SG1 episode 48 hours. as far as I know Atlantis's shield doesn't have that capability, for this story I'm saying that it does!</p>
    </blockquote></div><div class="userstuff module">
    
    <p>------</p>
<p>Sam isn’t exactly happy as she walks down the ramp out of the gate and into SGC. The spectre of her IOA review is hanging over her head, but even so it’s nice to be back into the familiar grey of SGC’s corridors. Even better, Jack is waiting at the bottom of the ramp to greet her. She’s just about to greet him when something else grabs her attention: Woolsy is walking past her, up the ramp. He disappears through the still open gate to Atlantis.</p>
<p>She frowns as she faces back to Jack, commenting:</p>
<p>“Woolsy going to Atlantis?”</p>
<p>That makes Jack look even more grim and she suddenly has a sinking feeling. She steps closer to him, trying not to let any of the panic seep into her voice:</p>
<p>“Jack, what’s wrong?”</p>
<p>He twitches slightly, that way he does before he delivers news he really doesn't want to be delivering. Then he straightens into his military posture and speaks clearly:</p>
<p>“Colonel Carter, I’m afraid that as of now, you are being relieved of your command of Atlantis.”</p>
<p>She can’t help but gasp; never in a million years could she have expected this. It’s enough that she can’t stop some of the hurt showing in her eyes.</p>
<p>He hesitates a moment before losing his sternness, becoming the commander she knows.</p>
<p>“Sam, I’m sorry.”</p>
<p>Suddenly; it all makes sense---the abruptness of the order for her to return, the request for her not to bring any Atlantis personal with her, Woolsy going through the gate. She spins as she hears the gate closing, watching as the iris slams shut, closing her off from the city she’s come to love, the people she’s come to love. She spins back to Jack, a desperation rising in her, more intense than she’s felt in years. More intense than the desperation of battle, this is because she’s losing her team. </p>
<p>“Jack, I didn’t even get a chance to say goodbye! Please, let me go back through one more time…”</p>
<p>He’s shaking his head, a look in his eye that she recognizes from years of hearing him  complain about being ordered around by military commanders who have no idea what it’s like being out in the field. He has his orders, but she knows Jack O’Neill always finds a way to twist those orders. She starts back up the ramp, placing herself in front of the iris, waiting.</p>
<p>“Jack, they’re my people. My responsibility.”</p>
<p>He smiles wryly at her; how often he’d been the one saying that. Finally, he sighs and nods at the booth to let her through.</p>
<p>She smiles at him thankfully, before sobering and giving him a look she hopes he’ll understand.</p>
<p>“I’ll be back soon.”</p>
<p>The gate opens and she walks as soon as the backwash is clear.</p>
<p>------</p>
<p>Sheppard watches Colonel Carter leave. She’s at the mercy of the IOA now, and he knows from Elizabeth that the IOA have very little mercy. He hopes she’ll be alright; he still misses Elizabeth, but Sam is a fiery, smart commander worth respecting. He’s turning away when he hears the strange noise of another person coming through the gate. Of all the people he might have consider coming through, he would never have expected Woolsey, standing there with his suit and a bulkier than usual briefcase.</p>
<p>But Woolsey is the IOA’s mouthpiece, so Sheppard steps forward to do his polite duty.</p>
<p>“Mr. Woolsey, we weren't expecting you. ”</p>
<p>He sighs, fingers tightening around the handle of the briefcase. Sheppard frowns; Woolsey is almost never nervous.</p>
<p>“Well, yes. I’m afraid I’ve brought some bad news.”</p>
<p>He straightens, looking at the entire gate room instead of just Sheppard, and raises his voice to speak so everyone can hear.</p>
<p>“I’m afraid Colonel Carter has been relieved of command and I am taking her place.”</p>
<p>The gate closes in the shocked silence. Woolsey shifts uncomfortably as the Atlantis crew looks at each other.  Sheppard, knowing everyone is looking at him to react first, tries to speak but only manages to stutter. Before he can find something to say, Chuck’s voice rings out across the room as the gate activates again:</p>
<p>“”Unscheduled offworld activation; SGC IDC.”</p>
<p>Woolsey suddenly looks shocked as well, and they all turn to stare at the gate. Colonel Carter comes through, her blue eyes blazing the same shade as the gate. She steps through, looking over her shocked crew and sheppard shrugs confusedly at her. She smiles reassuringly then changes back to wrathful, looking at Woolsey.</p>
<p>“Mr. Woolsey. They’re going to abandon Atlantis, aren’t they.”</p>
<p>Woolsey may be a tool of the IOA, but he’s been in the pegasus galaxy enough that it’s taken its hold on him like it has them, and he looks ashamed.</p>
<p>“Not quite correct, Colonel Carter.”</p>
<p>He raises the bulky briefcase and sheppard notices a warning label on it’s side.</p>
<p>“I was given an extra ZPM to bring Atlantis back to earth. To bring you home.”</p>
<p>Sam never would have thought those words would feel like such a slap to the face. Somehow this feels worse than just leaving Atlantis; they’ll be taking all of Atlantis's technology and knowledge with them and leaving a galaxy of vulnerable people behind. They would essentially be taking everything of value to them from Pegasus and leaving the people they’ve traded with---and promised protection to---for the last four years. The thought of such a complete betrayal of everything they’ve worked for makes her sick to her stomach.</p>
<p>Then Teyla pushes out of the crowd to address Woolsey, glowing with a rage even fiercer than Sam’s. She has so much more to lose, with her people on her mainland, halved by Michael’s experiments already. Sam thinks of Halling’s shaved head and haunted eyes, the scars on Kanan’s cheeks, thinks of leaving such a traumatized group of people at the mercy of the wraith. She thinks of M7G - 677, it’s children who had already faced so much and who always painted the faces of the lanteans who visited them. She thinks of how Ladon had finally come to them to ask for help with the radiation that was killing his people only a week ago.</p>
<p>She’s drawn out of her horrified thoughts when Teyla speaks, proud and regal, her voice ringing throughout the gate room for all to hear.</p>
<p>“So this what I have left my people for? What they have suffered for? What your own people have died for? When you came to us, you made many promises. You yourself looked me in the eye and promised me your people’s help, Mr. Woolsey. Your leader swore you would not abandon us. So we suffered and we died, because we believed we were fighting for a just cause. Is this all our loyalty and sacrifice has earned us?”</p>
<p>Woolsey is shrinking, the shame looking like it’s eating away at him from the inside.</p>
<p>“I don’t have a choice. This isn’t just from the IOA, it’s from the highest levels of the military. Even the president signed on.”</p>
<p>Teyla’s rage is spreading throughout the room, Ronon’s fingers flexing on the handle of his gun as he holds her hand in a deathly tight grip. The non earthers are shouting, eyes bright with desperation and disappointment. Even the earth people are beginning to mumble mutinously; Zelenka is spitting czech that she can’t understand at Woolsey, Rodney is ranting and waving his computer for emphasis. The military are calmer, but she can see the anger in the way they hold their guns. Lorne is next to Zelenka and Mckay, his mouth in a harsh line. Sheppard looks at her; his anger hidden but just as strong as Rodney or Teyla. </p>
<p>He is giving her that look he gives her before he asks her to break the rules to okay a mission, like he’s ready to fly a jumper into another suicide mission if it would stop this. She feels it too, the anger and betrayal humming in her blood and pushing her into action. She may regret this decision for the rest of her life, but she thinks she’d regret it more if she didn’t make it. Maybe they’ve gone native, gone space crazy, but pegasus feels like more a home than earth had.</p>
<p>So she steps forwards and shouts above the tumult:</p>
<p>“Quiet!”</p>
<p>They stop, and the silence makes her proud; they respect her and she respects them. She nods at Lorne and Sheppard as she speaks:</p>
<p>“Would you two please escort Mr. Woolsey to a cell?”</p>
<p>He stutters, absolutely shocked, but her soldiers don’t hesitate. Zelenka snatches the briefcase out of his hands as they remove him, the crowd snarling at him as he passes through them.  Rodney is squabbling with Zelenka like usual, trying to pull the latches open to get at the ZPM open as she snaps her next order at them: </p>
<p>“Get the ZPM plugged in and get Atlantis ready to fly.”</p>
<p>They look at her with faint surprise before scurrying off without complaint. The crowd is shifting, cautious hope in their eyes as they watch her.  Teyla and Ronon step closer, bracketing her,  and Teyla whispers to her:</p>
<p>“What is the plan, colonel?”</p>
<p>Sam laughs, a bit of hysteria to it. This has been a snap decision, but she’s committed now. She thinks maybe she knew she was even before she chased Woolsey back through the gate.</p>
<p>“I don’t know yet, Teyla. But I do know we’re getting out of here. Chuck; block any incoming gate activation, no matter who it is. They can send the Daedalus after us, but we’ll be cloaked on a new planet by the time they get here.”</p>
<p>————</p>
<p>She’s in the briefing room, the reality of what they’ve done just sinking in, when Rodney appears. He reports:</p>
<p>“We’re safely down on P8G- 634. There should be no way for them to track us. The shield has been inverted, preventing them from dialing in, though they’ve tried multiple times to do so.”</p>
<p>Sam nods, glad at least that they’ve found a safe planet to hide on. </p>
<p>“Thank you, Rodney.”</p>
<p>Rodney pauses, giving her a concerned look. </p>
<p>“You okay?”</p>
<p>She laughs, an edge of hysteria to it. </p>
<p>“What have I gotten us into, Rodney?”</p>
<p>Rodeny sits down next to her and complains:</p>
<p>“What have you gotten us into? I don’t remember any of us trying to stop you.”</p>
<p>She smiles weakly at him.</p>
<p>“That’s true.”</p>
<p>Rodney smiles back and continues:</p>
<p>“Seriously, Sam, this is what everyone wanted. Pegasus is our home now and we’re not leaving it because some politician decided we should.”</p>
<p>Sam sighs, buries her face in her hands for a long moment as she says:</p>
<p>“But Rodney, being cut off from earth means no more supplies. No food, no water, no ammo, no medical supplies.”</p>
<p>Rodney sighs too, and nods.</p>
<p>“I’m not denying it’s going to be difficult. But I believe we can do it.”</p>
<p>She nods, feeling stronger having someone else tell her they can do it, not just herself. She pushes a page of paper towards him and says:</p>
<p>“I think we can trade for ammo from the genaii, their guns are different than ours but with some modifications...”</p>
<p>--------<br/>Lorne and Sheppard are walking back from placing woolsey in unused quarters with a locked door---they had decided against putting him in one of the cells---when Lorne speaks up:</p>
<p>“We’re pretty fucked, aren’t we sir?”</p>
<p>Sheppard considers that before shrugging:</p>
<p>“I don’t think so.”</p>
<p>“Sir, we just collectively disobeyed an order that came directly from the president. If we ever try to go to earth again, we’ll be court martialed so fast our heads will spin.”</p>
<p>John considers longer this time before he says:</p>
<p>“True, but I still wouldn’t say we’re totally fucked.”</p>
<p>Lorne shakes his head, overwhelmed:</p>
<p>“The sheer logistics of trying to run this city without support...”</p>
<p>John cuts him off:</p>
<p>“Leave that to the big brains. Our job is to protect our people, even if that means protecting them from earth itself. Besides, we’ve never really been ones for following the rules, have we?”</p>
<p>Lorne smiles ruefully.</p>
<p>“No, sir.”</p>
<p>Sheppard pats him on the shoulder, sauntering back to the gate room.</p>
<p>“Cheer up. We’re on a grand ol’ adventure, let’s see where it leads.”</p>
<p>-----</p>
<p> </p>
<p>Sam sits in her office, looking through reports, when she hears someone enter the room. She looks up and smiles when she meets Ronon and Teyla’s eyes. </p>
<p>“Hello, Ronon, Teyla. What can I do for you.”</p>
<p>Ronon steps forwards and speaks, tone earnest:</p>
<p>“We wanted to say thank you. For not leaving us.”</p>
<p>Teyla nods and chimes in:</p>
<p>“You have sacrificed much to stay in pegasus and continue the fight against the wraith.”</p>
<p>Sam swallows, thinking of all the people she left on earth, Jack, Teal’c, Daniel…</p>
<p>“It was the right decision. I don’t regret it.”</p>
<p>Teyla and Ronon give her soft, grateful smiles, and Teyla says:</p>
<p>“We are glad.”</p>
<p>At that, Ronon turns to leave, but Teyla remains. Sam asks:</p>
<p>“You had more to discuss?”</p>
<p>“Yes. My people on the mainland understood why Atlantis had to leave immediately. Still, they would like to be transferred to this new planet’s mainland, as soon as it is possible.”</p>
<p>Sam can’t help but feel a little surprised.</p>
<p>“I thought they were well established there. Are they sure they want to leave that to start over here?”</p>
<p>Teyla gives her a sly smile.</p>
<p>“You have left a whole planet for us, Sam. We will leave a village of two seasons for you.”</p>
<p>Sam smiles back, touched.</p>
<p>“Very well. We will send jumpers for them as soon as possible.”</p>
<p>Teyla bows her head and says:</p>
<p>“Thank you, Sam.”</p>
<p>------</p>
<p>It’s been three years. There were lean times, times they had to ration and feared starvation, but they had survived. They had made many new allies by sending the gate teams out and soon were back to full strength. They are still fighting a war with the wraith, and aren't exactly winning, but it’s better than abandoning the pegasus galaxy. Sam is proud of her people, the hardship they’ve suffered without complaint, their bravery in the face of a great enemy.</p>
<p>She has become a leader in her own right. </p>
<p>That’s why she’s standing in front of the gate with a radio, preparing to talk to the SGC for the first time in three years.</p>
<p>She nods at Chuck and he adjusts the angle of the shield, pulling it back so the wormhole can form. Then he begins to dial. She tries to breathe deeply and calmly as the stargate spins. Once the wormhole settles into the puddle, she clicks the radio on and speaks into it:</p>
<p>“Stargate command, come in. This is Atlantis.”</p>
<p>There’s a long moment of silence and then a very surprised voice:</p>
<p>“This is Lt. Harriman, please repeat? Did you say this is Atlantis?”</p>
<p>Sam can’t help but smirk.</p>
<p>“This is Sam Carter of Atlantis. Yes, we’re still alive.”</p>
<p>The voice turns from surprised to cautious.</p>
<p>“Colonel Carter, may I ask why you’re calling.”</p>
<p>“I’m not a Colonel anymore, Lt. and that’s why I called. Just to let you know we survived and are doing fine. Please pass the message on, will you?”</p>
<p>A moment of hesitation, and then:</p>
<p>“Um, sure?”</p>
<p>“Thank you. ”</p>
<p>She cuts the radio transmission off and orders Chuck:</p>
<p>“Replace the shield to block incoming wormholes. We’ll keep it blocked for a few days, since they’ll probably try dialing us again.”</p>
<p>John is standing by the stairs as she ascend to her office and he asks:</p>
<p>“Feel better?”</p>
<p>She thinks of Jack, Daniel and Teal’c, finally receiving the news that she wasn’t dead.</p>
<p>“Yes, much better.”</p>
<p>With that she returns to her office and looks out over the gateroom, populated with her people, all working diligently at their assigned jobs. She’s proud of them, she really is. They’ve made Atlantis their home, all on their own. </p>
<p>-------</p>
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